Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01000764.1 Hibiscus syriacus cultivar Beakdansim tig00001486_pilon, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 27239
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:411 original size:36 final size:37

Alignment explanation


    Indices: 336--411  Score: 102
    Period size: 35  Copynumber: 2.1  Consensus size: 37

        326 CTTTTATATT

                                              *  
        336 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
          1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA

                          *                 *     
        373 TTTAATTTT-TAAAGAAAA-TATATAAATATTTTACAA
          1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA

               
        409 TTT
          1 TTT

        412 CTAATATTAT


Statistics
Matches: 35,  Mismatches: 3, Indels: 3
        0.85            0.07        0.07

Matches are distributed among these distances:
  35   13  0.37
  36   13  0.37
  37    9  0.26

ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46


Consensus pattern (37 bp):   
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA

Found at i:10142 original size:12 final size:13

Alignment explanation


    Indices: 10117--10145  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

      10107 AGTCAATAGG

                         
      10117 TTGACTCAACGAA
          1 TTGACTCAACGAA

                         
      10130 TTGACTC-ACGAA
          1 TTGACTCAACGAA

                
      10142 TTGA
          1 TTGA

      10146 ATCTACTGAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12    9  0.56
  13    7  0.44

ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28


Consensus pattern (13 bp):   
TTGACTCAACGAA

Found at i:11944 original size:41 final size:41

Alignment explanation


    Indices: 11899--11984  Score: 127
    Period size: 41  Copynumber: 2.1  Consensus size: 41

      11889 GCCTGGCCTG

                                             *  *    
      11899 GCCTATTTAACTAAACAAGCCAGGCCCAGGCCTTTTTAAAA
          1 GCCTATTTAACTAAACAAGCCAGGCCCAGGCCTATTAAAAA

                             *       **              
      11940 GCCTATTTAACTAAACATGCCAGGCTTAGGCCTATTAAAAA
          1 GCCTATTTAACTAAACAAGCCAGGCCCAGGCCTATTAAAAA

                
      11981 GCCT
          1 GCCT

      11985 TATAAGCCTG


Statistics
Matches: 40,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  41   40  1.00

ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26


Consensus pattern (41 bp):   
GCCTATTTAACTAAACAAGCCAGGCCCAGGCCTATTAAAAA

Found at i:13993 original size:22 final size:22

Alignment explanation


    Indices: 13937--13993  Score: 62
    Period size: 22  Copynumber: 2.6  Consensus size: 22

      13927 TTGTTTAGCC

                                  
      13937 AAGCCAAGTCGTTAAATCCTTT
          1 AAGCCAAGTCGTTAAATCCTTT

            *      **    *         
      13959 GAGCCAAACCGTTTAAT-CTTCT
          1 AAGCCAAGTCGTTAAATCCTT-T

                         
      13981 AAGCCAAGTCGTT
          1 AAGCCAAGTCGTT

      13994 GAATGAGCCG


Statistics
Matches: 27,  Mismatches: 7, Indels: 2
        0.75            0.19        0.06

Matches are distributed among these distances:
  21    3  0.11
  22   24  0.89

ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30


Consensus pattern (22 bp):   
AAGCCAAGTCGTTAAATCCTTT

Found at i:20068 original size:24 final size:24

Alignment explanation


    Indices: 20036--20086  Score: 59
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      20026 AAAATATACC

                *          *         
      20036 TAAAGTTTA-ATTTTGTTTCATATT
          1 TAAAATTTAGATTTTATTTCAT-TT

                      *             
      20060 TAAAATTTAGTTTTTATTTCATTT
          1 TAAAATTTAGATTTTATTTCATTT

               
      20084 TAA
          1 TAA

      20087 TACACGCCGT


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  24   13  0.57
  25   10  0.43

ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59


Consensus pattern (24 bp):   
TAAAATTTAGATTTTATTTCATTT

Found at i:20166 original size:19 final size:20

Alignment explanation


    Indices: 20126--20168  Score: 61
    Period size: 20  Copynumber: 2.2  Consensus size: 20

      20116 TTGACATGGT

                *          *    
      20126 ATTTTTAAATTATTTTTTTA
          1 ATTTATAAATTATTTATTTA

                                
      20146 ATTTATAAATTA-TTATTTA
          1 ATTTATAAATTATTTATTTA

                
      20165 ATTT
          1 ATTT

      20169 TTTTTATTCC


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  19   10  0.48
  20   11  0.52

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (20 bp):   
ATTTATAAATTATTTATTTA
Done.